Dingpf/packaging

.github/workflows/CI_python.yaml

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+name: Python Code Checks
+
+on:
+  workflow_dispatch:
+  push:
+    branches:
+      - main
+  pull_request:
+    branches:
+      - main
+
+jobs:
+  test:
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: Checkout code
+        uses: actions/checkout@v2
+
+      - name: Set up Python
+        uses: actions/setup-python@v2
+        with:
+          python-version: '3.11'
+
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          cd ./hmatools
+          python -m pip install --use-pep517 -e .
+          python -m pip install black flake8 pylint mypy pytest
+          python -m pip install types-seaborn pandas-stubs matplotlib-stubs
+
+      - name: Format code with Black
+        run: |
+          cd ./hmatools/python
+          black --check .
+
+      - name: Lint with Flake8
+        run: |
+          cd ./hmatools/python
+          flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
+          flake8 . --count --exit-zero --max-complexity=10 --max-line-length=100 --statistics
+
+      - name: Lint with Pylint
+        run: |
+          cd ./hmatools/python
+          pylint .
+
+      - name: Type check with Mypy
+        run: |
+          cd ./hmatools/python
+          mypy . --explicit-package-bases
+
+      - name: Run tests
+        run: |
+          pytest

.github/workflows/OVERVIEW.md

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+# GitHub Actions Workflows Overview
+
+## 1. Run FastCaloSim Benchmarking (`benchmarking.yaml`)
+
+The `benchmarking.yaml` workflow is designed to automate the benchmarking of FastCaloSim on different environments, including Perlmutter and Exalearn. Steps:
+
+- **Build and Push Images**:
+  - This step is optional and controlled via workflow dispatch (`run_build` input).
+  - If triggered, the job builds and pushes Docker images using a self-hosted runner, and logs are uploaded for review.
+
+- **Run FastCaloSim**:
+  - This job runs FastCaloSim on different platforms using a matrix strategy to handle multiple configurations (Perlmutter and Exalearn).
+  - It sets up environment variables specific to each runner and executes the simulation scripts.
+  - Log files from each run are compressed into tarballs and uploaded for later use.
+
+- **Postprocess Log Files**:
+  - This job depends on the completion of the `run` job.
+  - It downloads log files from the previous runs, decompresses them, and runs a postprocessing script using HMATools.
+  - The processed logs and resulting JSON files are uploaded as artifacts.
+
+- **Plot Results**:
+  - This job depends on the completion of the `postprocess` job.
+  - It downloads the processed JSON files and runs a plotting script using HMATools.
+  - The generated plots and associated logs are uploaded for analysis.
+
+For postprocessing, and plotting, a docker container with HMATools is built and run to execute the steps.
+
+## 2. Python Code Checks (`Python_CI.yaml`)
+
+The `Python_CI.yaml` workflow is a Continuous Integration (CI) pipeline focused on ensuring code quality and correctness in the HMATools project. It includes the following steps:
+
+- **Checkout Code**:
+  - The repository is checked out to the runner for subsequent operations.
+
+- **Set Up Python**:
+  - Python 3.11 is installed and configured for the environment.
+
+- **Install Dependencies**:
+  - All necessary Python packages, including project dependencies and development tools like `black`, `flake8`, `pylint`, `mypy`, and `pytest`, are installed.
+
+- **Code Formatting with Black**:
+  - The codebase is checked for compliance with `black` formatting standards.
+
+- **Linting with Flake8 and Pylint**:
+  - Code is linted to catch syntax errors, enforce coding standards, and assess code complexity.
+
+- **Type Checking with Mypy**:
+  - Static type checking is performed to catch type-related errors before runtime.
+
+- **Run Tests**:
+  - Unit tests are executed using `pytest` to ensure the functionality is working as expected.

.github/workflows/benchmarking.yaml

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+name: Run FastCaloSim Benchmarking
+
+on:
+  workflow_dispatch:
+
+  push:
+    branches:
+      - main
+  pull_request:
+    branches:
+      - main
+
+jobs:
+  run:
+    runs-on: ${{ matrix.runner-label }}
+    name: Run FastCaloSim
+    strategy:
+      matrix:
+        runner-label: [pm-login, exalearn5]
+    env:
+      LOG_DIR: ${{ github.workspace }}/logs/run
+      NERSC_CONTAINER_REGISTRY_USER: ${{ secrets.NERSC_CONTAINER_REGISTRY_USER }}
+      NERSC_CONTAINER_REGISTRY_PASSWORD: ${{ secrets.NERSC_CONTAINER_REGISTRY_PASSWORD }}
+
+    steps:
+    - name: Checkout repository
+      uses: actions/checkout@v4
+
+    - name: Run FastCaloSim on Perlmutter
+      if: contains(runner.name, 'pm-login')
+      env:
+        RUNNER_LABEL: pm-login
+        FCS_DATAPATH: /global/cfs/cdirs/atlas/leggett/data/FastCaloSimInputs
+      run: |
+        cd ./scripts/run_scripts
+        ./run_images.sh
+
+    - name: Run FastCaloSim on exalearn5
+      if: contains(runner.name, 'exalearn5')
+      env:
+        RUNNER_LABEL: exalearn5
+        FCS_DATAPATH: /local/scratch/cgleggett/data/FastCaloSimInputs
+      run: |
+        cd ./scripts/run_scripts
+        ./run_images.sh
+
+    - name: Create tarball of log files
+      run: |
+        cd ${{ env.LOG_DIR }}
+        tar -czf ${{ github.workspace }}/log_files_${{ matrix.runner-label }}.tar.gz ./*.txt
+
+    - name: Upload log files
+      uses: actions/upload-artifact@v4
+      with:
+        name: Log Files - ${{ matrix.runner-label }}
+        path: log_files_${{ matrix.runner-label }}.tar.gz
+
+  postprocess:
+    runs-on: ubuntu-latest
+    name: Postprocess log files
+    needs: run
+    env:
+      LOG_DIR: ${{ github.workspace }}/logs/postprocess
+      INPUT_DIR: ${{ github.workspace }}/logs/run
+      OUTPUT_DIR: ${{ github.workspace }}/logs/postprocess
+      SCRIPT: ./postprocess.sh
+
+    steps:
+    - name: Checkout repository
+      uses: actions/checkout@v4
+
+    - name: Download pm-login log files
+      uses: actions/download-artifact@v4
+      with:
+        name: Log Files - pm-login
+        path: ${{ env.INPUT_DIR }}
+
+    - name: Download exalearn5 log files
+      uses: actions/download-artifact@v4
+      with:
+        name: Log Files - exalearn5
+        path: ${{ env.INPUT_DIR }}
+
+    - name: Untar and uncompress logs
+      run: |
+        for runner in pm-login exalearn5; do
+          tar -xzf ${{ github.workspace }}/logs/run/log_files_${runner}.tar.gz -C ${{ github.workspace }}/logs/run
+        done
+
+    - name: Debug input directory
+      run: |
+        ls -l ${{ env.INPUT_DIR }}
+
+    - name: Build hmatools image
+      run: |
+        cd ./hmatools/scripts
+        ./build_image.sh
+
+    - name: Run hmatools postprocessing
+      run: |
+        cd ./hmatools/scripts
+        ./run_image.sh
+
+    - name: Upload logfiles
+      if: always()
+      uses: actions/upload-artifact@v4
+      with:
+        name: Postprocess log file
+        path: ${{ env.LOG_DIR }}/*.txt
+
+    - name: Upload json files
+      if: always()
+      uses: actions/upload-artifact@v4
+      with:
+        name: FastCaloSim Results (JSON)
+        path: ${{ env.OUTPUT_DIR }}/*.json
+
+    - name: Cleanup workspace
+      run: rm -rf ${{ github.workspace }}/*
+
+  plot:
+    runs-on: ubuntu-latest
+    name: Plot results
+    needs: postprocess
+    env:
+      LOG_DIR: ${{ github.workspace }}/logs/plot
+      INPUT_DIR: ${{ github.workspace }}/logs/postprocess
+      OUTPUT_DIR: ${{ github.workspace }}/logs/plot
+      SCRIPT: ./plot.sh
+
+    steps:
+    - name: Checkout repository
+      uses: actions/checkout@v4
+
+    - name: Download json files
+      uses: actions/download-artifact@v4
+      with:
+        name: FastCaloSim Results (JSON)
+        path: ${{ env.INPUT_DIR }}
+
+    - name: Debug input directory
+      run: |
+        ls -l ${{ env.INPUT_DIR }}
+
+    - name: Build hmatools image
+      run: |
+        cd ./hmatools/scripts
+        ./build_image.sh
+
+    - name: Run hmatools plotting
+      run: |
+        cd ./hmatools/scripts
+        ./run_image.sh
+
+    - name: Upload logfiles
+      if: always()
+      uses: actions/upload-artifact@v4
+      with:
+        name: Plot log file
+        path: ${{ env.LOG_DIR }}/*.txt
+
+    - name: Upload plot files
+      if: always()
+      uses: actions/upload-artifact@v4
+      with:
+        name: Result plots
+        path: ${{ env.OUTPUT_DIR }}/*.png

.github/workflows/build_image.yaml

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+name: Build Container images with FastCaloSim
+
+on:
+  workflow_dispatch:
+    inputs:
+      run_build:
+        description: "Run the build job?"
+        required: false
+        default: "false"
+  push:
+    branches:
+      - main
+  pull_request:
+    branches:
+      - main
+
+jobs:
+  build:
+    runs-on: [self-hosted, pm-login]
+    name: Build and push images
+    if: ${{ github.event.inputs.run_build == 'true' }}
+    env:
+      LOG_DIR: ${{ github.workspace }}/logs/build
+
+    steps:
+    - name: Checkout repository
+      uses: actions/checkout@v4
+
+    - name: Build images
+      run: |
+        cd ./scripts/build_scripts
+        ./build_images.sh
+
+    - name: Upload log files
+      uses: actions/upload-artifact@v4
+      with:
+        name: Log File - Building and Pushing container images
+        path: ${{ env.LOG_DIR }}/*.txt
+
+    - name: Cleanup workspace
+      run: rm -rf ${{ github.workspace }}/*

.gitignore

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+**/.DS_Store
+**/__pycache__/
+**/*.egg-info/
+**/json/**/*
+scripts/run_scripts/*.txt
+**/*.txt
+**/*.json
+**/*.png
+**/*.ipynb
+!/hmatools/tests/test_data/**
+!/hmatools/requirements.txt